2 // FORESTER -- software libraries and applications
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3 // for evolutionary biology research and applications.
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5 // Copyright (C) 2008-2009 Christian M. Zmasek
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6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
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7 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
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8 // All rights reserved
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10 // This library is free software; you can redistribute it and/or
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11 // modify it under the terms of the GNU Lesser General Public
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12 // License as published by the Free Software Foundation; either
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13 // version 2.1 of the License, or (at your option) any later version.
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15 // This library is distributed in the hope that it will be useful,
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16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
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17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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18 // Lesser General Public License for more details.
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20 // You should have received a copy of the GNU Lesser General Public
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21 // License along with this library; if not, write to the Free Software
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22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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24 // Contact: phylosoft @ gmail . com
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25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
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27 package org.forester.archaeopteryx;
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29 import java.awt.BorderLayout;
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30 import java.awt.Font;
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31 import java.awt.event.ActionEvent;
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32 import java.awt.event.ComponentAdapter;
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33 import java.awt.event.ComponentEvent;
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34 import java.awt.event.WindowAdapter;
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35 import java.awt.event.WindowEvent;
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36 import java.io.File;
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37 import java.io.FileInputStream;
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38 import java.io.IOException;
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39 import java.io.InputStream;
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40 import java.net.MalformedURLException;
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41 import java.net.URL;
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42 import java.util.ArrayList;
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43 import java.util.HashSet;
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44 import java.util.List;
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45 import java.util.Set;
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47 import javax.swing.ButtonGroup;
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48 import javax.swing.JCheckBoxMenuItem;
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49 import javax.swing.JFileChooser;
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50 import javax.swing.JMenu;
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51 import javax.swing.JMenuBar;
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52 import javax.swing.JMenuItem;
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53 import javax.swing.JOptionPane;
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54 import javax.swing.JRadioButtonMenuItem;
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55 import javax.swing.UIManager;
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56 import javax.swing.UnsupportedLookAndFeelException;
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57 import javax.swing.WindowConstants;
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58 import javax.swing.event.ChangeEvent;
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59 import javax.swing.event.ChangeListener;
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60 import javax.swing.plaf.synth.SynthLookAndFeel;
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62 import org.forester.analysis.TaxonomyDataManager;
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63 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
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64 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
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65 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
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66 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
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67 import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
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68 import org.forester.archaeopteryx.tools.InferenceManager;
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69 import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
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70 import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
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71 import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
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72 import org.forester.archaeopteryx.tools.SequenceDataRetriver;
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73 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
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74 import org.forester.archaeopteryx.webservices.WebservicesManager;
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75 import org.forester.io.parsers.FastaParser;
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76 import org.forester.io.parsers.GeneralMsaParser;
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77 import org.forester.io.parsers.PhylogenyParser;
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78 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
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79 import org.forester.io.parsers.nhx.NHXParser;
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80 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
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81 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
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82 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
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83 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
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84 import org.forester.io.parsers.tol.TolParser;
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85 import org.forester.io.parsers.util.ParserUtils;
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86 import org.forester.io.writers.PhylogenyWriter;
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87 import org.forester.io.writers.SequenceWriter;
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88 import org.forester.msa.Msa;
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89 import org.forester.msa.MsaFormatException;
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90 import org.forester.phylogeny.Phylogeny;
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91 import org.forester.phylogeny.PhylogenyMethods;
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92 import org.forester.phylogeny.PhylogenyNode;
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93 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
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94 import org.forester.phylogeny.data.Confidence;
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95 import org.forester.phylogeny.data.PhylogenyDataUtil;
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96 import org.forester.phylogeny.data.Sequence;
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97 import org.forester.phylogeny.data.Taxonomy;
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98 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
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99 import org.forester.phylogeny.factories.PhylogenyFactory;
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100 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
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101 import org.forester.sequence.MolecularSequence;
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102 import org.forester.util.BasicDescriptiveStatistics;
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103 import org.forester.util.BasicTable;
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104 import org.forester.util.BasicTableParser;
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105 import org.forester.util.DescriptiveStatistics;
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106 import org.forester.util.ForesterUtil;
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108 public final class MainFrameApplication extends MainFrame {
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110 public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
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111 return new MainFrameApplication( phys, config );
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114 static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {
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115 return new MainFrameApplication( phys, config, title );
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118 public static MainFrame createInstance( final Phylogeny[] phys,
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119 final Configuration config,
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120 final String title,
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121 final File current_dir ) {
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122 return new MainFrameApplication( phys, config, title, current_dir );
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125 static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
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126 return new MainFrameApplication( phys, config_file_name, title );
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129 static void warnIfNotPhyloXmlValidation( final Configuration c ) {
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130 if ( !c.isValidatePhyloXmlAgainstSchema() ) {
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132 .showMessageDialog( null,
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134 .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
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137 JOptionPane.WARNING_MESSAGE );
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140 static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";
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141 static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";
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142 private final static int FRAME_X_SIZE = 800;
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143 private final static int FRAME_Y_SIZE = 800;
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144 // Filters for the file-open dialog (classes defined in this file)
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145 private static final long serialVersionUID = -799735726778865234L;
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146 private static final boolean PREPROCESS_TREES = false;
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147 private final JFileChooser _values_filechooser;
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148 private final JFileChooser _sequences_filechooser;
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149 private final JFileChooser _open_filechooser;
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150 private final JFileChooser _msa_filechooser;
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151 private final JFileChooser _seqs_pi_filechooser;
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152 private final JFileChooser _open_filechooser_for_species_tree;
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153 // Application-only print menu items
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154 private JMenuItem _collapse_below_threshold;
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155 private JMenuItem _collapse_below_branch_length;
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156 private ButtonGroup _radio_group_1;
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157 private ButtonGroup _radio_group_2;
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159 double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;
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160 double _min_not_collapse_bl = 0.001;
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161 // Phylogeny Inference menu
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162 private JMenu _inference_menu;
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163 private JMenuItem _inference_from_msa_item;
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164 private JMenuItem _inference_from_seqs_item;
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165 // Phylogeny Inference
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166 private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;
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167 private Msa _msa = null;
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168 private File _msa_file = null;
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169 private List<MolecularSequence> _seqs = null;
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170 private File _seqs_file = null;
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171 JMenuItem _read_values_jmi;
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172 JMenuItem _read_seqs_jmi;
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174 private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {
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175 _configuration = config;
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176 if ( _configuration == null ) {
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177 throw new IllegalArgumentException( "configuration is null" );
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179 setVisible( false );
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180 setOptions( Options.createInstance( _configuration ) );
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181 _mainpanel = new MainPanel( _configuration, this );
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182 _open_filechooser = null;
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183 _open_filechooser_for_species_tree = null;
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184 _save_filechooser = null;
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185 _writetopdf_filechooser = null;
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186 _writetographics_filechooser = null;
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187 _msa_filechooser = null;
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188 _seqs_pi_filechooser = null;
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189 _values_filechooser = null;
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190 _sequences_filechooser = null;
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191 _jmenubar = new JMenuBar();
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194 _contentpane = getContentPane();
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195 _contentpane.setLayout( new BorderLayout() );
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196 _contentpane.add( _mainpanel, BorderLayout.CENTER );
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198 setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
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199 // The window listener
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200 setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
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201 addWindowListener( new WindowAdapter() {
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204 public void windowClosing( final WindowEvent e ) {
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208 // setVisible( true );
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209 if ( ( phys != null ) && ( phys.length > 0 ) ) {
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210 AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel );
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212 getMainPanel().getControlPanel().showWholeAll();
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213 getMainPanel().getControlPanel().showWhole();
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215 //activateSaveAllIfNeeded();
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216 // ...and its children
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217 _contentpane.repaint();
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220 private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {
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221 this( phys, config, title, null );
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224 private MainFrameApplication( final Phylogeny[] phys,
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225 final Configuration config,
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226 final String title,
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227 final File current_dir ) {
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229 _configuration = config;
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230 if ( _configuration == null ) {
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231 throw new IllegalArgumentException( "configuration is null" );
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234 boolean synth_exception = false;
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235 if ( Constants.__SYNTH_LF ) {
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237 final SynthLookAndFeel synth = new SynthLookAndFeel();
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238 synth.load( MainFrameApplication.class.getResourceAsStream( "/resources/synth_look_and_feel_1.xml" ),
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239 MainFrameApplication.class );
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240 UIManager.setLookAndFeel( synth );
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242 catch ( final Exception ex ) {
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243 synth_exception = true;
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244 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
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245 "could not create synth look and feel: "
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246 + ex.getLocalizedMessage() );
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249 if ( !Constants.__SYNTH_LF || synth_exception ) {
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250 if ( _configuration.isUseNativeUI() ) {
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251 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
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254 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
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257 //UIManager.setLookAndFeel( "com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel" );
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259 catch ( final UnsupportedLookAndFeelException e ) {
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260 AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() );
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262 catch ( final ClassNotFoundException e ) {
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263 AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() );
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265 catch ( final InstantiationException e ) {
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266 AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() );
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268 catch ( final IllegalAccessException e ) {
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269 AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );
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271 if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
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272 setCurrentDir( current_dir );
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274 // hide until everything is ready
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275 setVisible( false );
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276 setOptions( Options.createInstance( _configuration ) );
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277 setInferenceManager( InferenceManager.createInstance( _configuration ) );
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278 setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );
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279 // _textframe = null; #~~~~
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281 setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" );
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282 _mainpanel = new MainPanel( _configuration, this );
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283 // The file dialogs
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284 _open_filechooser = new JFileChooser();
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285 _open_filechooser.setCurrentDirectory( new File( "." ) );
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286 _open_filechooser.setMultiSelectionEnabled( false );
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287 _open_filechooser.addChoosableFileFilter( MainFrame.xmlfilter );
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288 _open_filechooser.addChoosableFileFilter( MainFrame.nhxfilter );
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289 _open_filechooser.addChoosableFileFilter( MainFrame.nhfilter );
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290 _open_filechooser.addChoosableFileFilter( MainFrame.nexusfilter );
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291 _open_filechooser.addChoosableFileFilter( MainFrame.tolfilter );
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292 _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() );
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293 _open_filechooser.setFileFilter( MainFrame.defaultfilter );
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294 _open_filechooser_for_species_tree = new JFileChooser();
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295 _open_filechooser_for_species_tree.setCurrentDirectory( new File( "." ) );
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296 _open_filechooser_for_species_tree.setMultiSelectionEnabled( false );
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297 _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.xmlfilter );
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298 _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.tolfilter );
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299 _open_filechooser_for_species_tree.setFileFilter( MainFrame.xmlfilter );
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300 _save_filechooser = new JFileChooser();
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301 _save_filechooser.setCurrentDirectory( new File( "." ) );
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302 _save_filechooser.setMultiSelectionEnabled( false );
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303 _save_filechooser.setFileFilter( MainFrame.xmlfilter );
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304 _save_filechooser.addChoosableFileFilter( MainFrame.nhfilter );
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305 _save_filechooser.addChoosableFileFilter( MainFrame.nexusfilter );
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306 _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
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307 _writetopdf_filechooser = new JFileChooser();
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308 _writetopdf_filechooser.addChoosableFileFilter( MainFrame.pdffilter );
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309 _writetographics_filechooser = new JFileChooser();
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310 _writetographics_filechooser.addChoosableFileFilter( MainFrame.graphicsfilefilter );
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312 _msa_filechooser = new JFileChooser();
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313 _msa_filechooser.setName( "Read Multiple Sequence Alignment File" );
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314 _msa_filechooser.setCurrentDirectory( new File( "." ) );
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315 _msa_filechooser.setMultiSelectionEnabled( false );
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316 _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );
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317 _msa_filechooser.addChoosableFileFilter( MainFrame.msafilter );
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319 _seqs_pi_filechooser = new JFileChooser();
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320 _seqs_pi_filechooser.setName( "Read Sequences File" );
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321 _seqs_pi_filechooser.setCurrentDirectory( new File( "." ) );
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322 _seqs_pi_filechooser.setMultiSelectionEnabled( false );
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323 _seqs_pi_filechooser.addChoosableFileFilter( _seqs_pi_filechooser.getAcceptAllFileFilter() );
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324 _seqs_pi_filechooser.addChoosableFileFilter( MainFrame.seqsfilter );
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326 _values_filechooser = new JFileChooser();
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327 _values_filechooser.setCurrentDirectory( new File( "." ) );
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328 _values_filechooser.setMultiSelectionEnabled( false );
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330 _sequences_filechooser = new JFileChooser();
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331 _sequences_filechooser.setCurrentDirectory( new File( "." ) );
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332 _sequences_filechooser.setMultiSelectionEnabled( false );
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333 // build the menu bar
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334 _jmenubar = new JMenuBar();
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335 if ( !_configuration.isUseNativeUI() ) {
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336 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
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339 if ( Constants.__ALLOW_PHYLOGENETIC_INFERENCE ) {
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340 buildPhylogeneticInferenceMenu();
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342 buildAnalysisMenu();
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345 buildFontSizeMenu();
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346 buildOptionsMenu();
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349 setJMenuBar( _jmenubar );
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350 _jmenubar.add( _help_jmenu );
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351 _contentpane = getContentPane();
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352 _contentpane.setLayout( new BorderLayout() );
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353 _contentpane.add( _mainpanel, BorderLayout.CENTER );
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355 setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
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356 // addWindowFocusListener( new WindowAdapter() {
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359 // public void windowGainedFocus( WindowEvent e ) {
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360 // requestFocusInWindow();
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363 // The window listener
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364 setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
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365 addWindowListener( new WindowAdapter() {
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368 public void windowClosing( final WindowEvent e ) {
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369 if ( isUnsavedDataPresent() ) {
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370 final int r = JOptionPane.showConfirmDialog( null,
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371 "Exit despite potentially unsaved changes?",
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373 JOptionPane.YES_NO_OPTION );
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374 if ( r != JOptionPane.YES_OPTION ) {
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379 final int r = JOptionPane.showConfirmDialog( null,
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380 "Exit Archaeopteryx?",
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382 JOptionPane.YES_NO_OPTION );
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383 if ( r != JOptionPane.YES_OPTION ) {
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390 // The component listener
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391 addComponentListener( new ComponentAdapter() {
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394 public void componentResized( final ComponentEvent e ) {
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395 if ( _mainpanel.getCurrentTreePanel() != null ) {
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396 _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()
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398 _mainpanel.getCurrentTreePanel()
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403 requestFocusInWindow();
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404 // addKeyListener( this );
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405 setVisible( true );
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406 if ( ( phys != null ) && ( phys.length > 0 ) ) {
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407 AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
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409 getMainPanel().getControlPanel().showWholeAll();
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410 getMainPanel().getControlPanel().showWhole();
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412 activateSaveAllIfNeeded();
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413 // ...and its children
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414 _contentpane.repaint();
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418 private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {
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419 // Reads the config file (false, false => not url, not applet):
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420 this( phys, new Configuration( config_file, false, false, true ), title );
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424 public void actionPerformed( final ActionEvent e ) {
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426 super.actionPerformed( e );
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427 final Object o = e.getSource();
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428 // Handle app-specific actions here:
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429 if ( o == _open_item ) {
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430 readPhylogeniesFromFile();
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432 if ( o == _open_url_item ) {
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433 readPhylogeniesFromURL();
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435 else if ( o == _new_item ) {
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439 else if ( o == _close_item ) {
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440 closeCurrentPane();
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443 else if ( o == _load_species_tree_item ) {
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444 readSpeciesTreeFromFile();
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446 else if ( o == _lineage_inference ) {
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447 if ( isSubtreeDisplayed() ) {
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448 JOptionPane.showMessageDialog( this,
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449 "Subtree is shown.",
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450 "Cannot infer ancestral taxonomies",
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451 JOptionPane.ERROR_MESSAGE );
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454 executeLineageInference();
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456 else if ( o == _obtain_detailed_taxonomic_information_jmi ) {
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457 if ( isSubtreeDisplayed() ) {
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460 obtainDetailedTaxonomicInformation();
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462 else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {
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463 if ( isSubtreeDisplayed() ) {
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466 obtainDetailedTaxonomicInformationDelete();
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468 else if ( o == _obtain_seq_information_jmi ) {
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469 obtainSequenceInformation();
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471 else if ( o == _read_values_jmi ) {
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472 if ( isSubtreeDisplayed() ) {
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475 addExpressionValuesFromFile();
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477 else if ( o == _read_seqs_jmi ) {
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478 if ( isSubtreeDisplayed() ) {
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481 addSequencesFromFile();
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483 else if ( o == _move_node_names_to_tax_sn_jmi ) {
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484 moveNodeNamesToTaxSn();
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486 else if ( o == _move_node_names_to_seq_names_jmi ) {
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487 moveNodeNamesToSeqNames();
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489 else if ( o == _extract_tax_code_from_node_names_jmi ) {
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490 extractTaxDataFromNodeNames();
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492 else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {
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493 updateOptions( getOptions() );
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495 else if ( o == _replace_underscores_cbmi ) {
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496 if ( ( _extract_taxonomy_no_rbmi != null ) && !_extract_taxonomy_no_rbmi.isSelected() ) {
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497 _extract_taxonomy_no_rbmi.setSelected( true );
\r
499 updateOptions( getOptions() );
\r
501 else if ( o == _allow_errors_in_distance_to_parent_cbmi ) {
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502 updateOptions( getOptions() );
\r
504 else if ( o == _collapse_below_threshold ) {
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505 if ( isSubtreeDisplayed() ) {
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508 collapseBelowThreshold();
\r
510 else if ( o == _collapse_below_branch_length ) {
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511 if ( isSubtreeDisplayed() ) {
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514 collapseBelowBranchLengthThreshold();
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516 else if ( ( o == _extract_taxonomy_pfam_strict_rbmi ) || ( o == _extract_taxonomy_pfam_relaxed_rbmi )
\r
517 || ( o == _extract_taxonomy_agressive_rbmi ) ) {
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518 if ( _replace_underscores_cbmi != null ) {
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519 _replace_underscores_cbmi.setSelected( false );
\r
521 updateOptions( getOptions() );
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523 else if ( o == _extract_taxonomy_no_rbmi ) {
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524 updateOptions( getOptions() );
\r
526 else if ( o == _inference_from_msa_item ) {
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527 executePhyleneticInference( false );
\r
529 else if ( o == _inference_from_seqs_item ) {
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530 executePhyleneticInference( true );
\r
532 _contentpane.repaint();
\r
534 catch ( final Exception ex ) {
\r
535 AptxUtil.unexpectedException( ex );
\r
537 catch ( final Error err ) {
\r
538 AptxUtil.unexpectedError( err );
\r
542 private void addExpressionValuesFromFile() {
\r
543 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
\r
544 JOptionPane.showMessageDialog( this,
\r
545 "Need to load evolutionary tree first",
\r
546 "Can Not Read Expression Values",
\r
547 JOptionPane.WARNING_MESSAGE );
\r
550 final File my_dir = getCurrentDir();
\r
551 if ( my_dir != null ) {
\r
552 _values_filechooser.setCurrentDirectory( my_dir );
\r
554 final int result = _values_filechooser.showOpenDialog( _contentpane );
\r
555 final File file = _values_filechooser.getSelectedFile();
\r
556 if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
557 BasicTable<String> t = null;
\r
559 t = BasicTableParser.parse( file, '\t' );
\r
560 if ( t.getNumberOfColumns() < 2 ) {
\r
561 t = BasicTableParser.parse( file, ',' );
\r
563 if ( t.getNumberOfColumns() < 2 ) {
\r
564 t = BasicTableParser.parse( file, ' ' );
\r
567 catch ( final IOException e ) {
\r
568 JOptionPane.showMessageDialog( this,
\r
570 "Could Not Read Expression Value Table",
\r
571 JOptionPane.ERROR_MESSAGE );
\r
574 if ( t.getNumberOfColumns() < 2 ) {
\r
575 JOptionPane.showMessageDialog( this,
\r
576 "Table contains " + t.getNumberOfColumns() + " column(s)",
\r
577 "Problem with Expression Value Table",
\r
578 JOptionPane.ERROR_MESSAGE );
\r
581 if ( t.getNumberOfRows() < 1 ) {
\r
582 JOptionPane.showMessageDialog( this,
\r
583 "Table contains zero rows",
\r
584 "Problem with Expression Value Table",
\r
585 JOptionPane.ERROR_MESSAGE );
\r
588 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
589 if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
\r
590 JOptionPane.showMessageDialog( this,
\r
591 "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
\r
592 + phy.getNumberOfExternalNodes() + " external nodes",
\r
594 JOptionPane.WARNING_MESSAGE );
\r
596 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
\r
598 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
\r
599 final PhylogenyNode node = iter.next();
\r
600 final String node_name = node.getName();
\r
601 if ( !ForesterUtil.isEmpty( node_name ) ) {
\r
604 row = t.findRow( node_name );
\r
606 catch ( final IllegalArgumentException e ) {
\r
608 .showMessageDialog( this,
\r
610 "Error Mapping Node Identifiers to Expression Value Identifiers",
\r
611 JOptionPane.ERROR_MESSAGE );
\r
615 if ( node.isExternal() ) {
\r
620 final List<Double> l = new ArrayList<Double>();
\r
621 for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
\r
624 d = Double.parseDouble( t.getValueAsString( col, row ) );
\r
626 catch ( final NumberFormatException e ) {
\r
627 JOptionPane.showMessageDialog( this,
\r
628 "Could not parse \"" + t.getValueAsString( col, row )
\r
629 + "\" into a decimal value",
\r
630 "Issue with Expression Value Table",
\r
631 JOptionPane.ERROR_MESSAGE );
\r
634 stats.addValue( d );
\r
637 if ( !l.isEmpty() ) {
\r
638 if ( node.getNodeData().getProperties() != null ) {
\r
639 node.getNodeData().getProperties()
\r
640 .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
\r
642 node.getNodeData().setVector( l );
\r
646 if ( not_found > 0 ) {
\r
647 JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
\r
648 + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
\r
650 getCurrentTreePanel().setStatisticsForExpressionValues( stats );
\r
654 private void addSequencesFromFile() {
\r
655 if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
\r
656 JOptionPane.showMessageDialog( this,
\r
657 "Need to load evolutionary tree first",
\r
658 "Can Not Read Sequences",
\r
659 JOptionPane.WARNING_MESSAGE );
\r
662 final File my_dir = getCurrentDir();
\r
663 if ( my_dir != null ) {
\r
664 _sequences_filechooser.setCurrentDirectory( my_dir );
\r
666 final int result = _sequences_filechooser.showOpenDialog( _contentpane );
\r
667 final File file = _sequences_filechooser.getSelectedFile();
\r
668 List<MolecularSequence> seqs = null;
\r
669 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
671 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
\r
672 seqs = FastaParser.parse( new FileInputStream( file ) );
\r
675 JOptionPane.showMessageDialog( this,
\r
676 "Format does not appear to be Fasta",
\r
677 "Multiple sequence file format error",
\r
678 JOptionPane.ERROR_MESSAGE );
\r
682 catch ( final MsaFormatException e ) {
\r
684 JOptionPane.showMessageDialog( this,
\r
685 e.getLocalizedMessage(),
\r
686 "Multiple sequence file format error",
\r
687 JOptionPane.ERROR_MESSAGE );
\r
690 catch ( final IOException e ) {
\r
692 JOptionPane.showMessageDialog( this,
\r
693 e.getLocalizedMessage(),
\r
694 "Failed to read multiple sequence file",
\r
695 JOptionPane.ERROR_MESSAGE );
\r
698 catch ( final Exception e ) {
\r
700 e.printStackTrace();
\r
701 JOptionPane.showMessageDialog( this,
\r
702 e.getLocalizedMessage(),
\r
703 "Unexpected error during reading of multiple sequence file",
\r
704 JOptionPane.ERROR_MESSAGE );
\r
707 if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
\r
708 JOptionPane.showMessageDialog( this,
\r
709 "Multiple sequence file is empty",
\r
710 "Empty multiple sequence file",
\r
711 JOptionPane.ERROR_MESSAGE );
\r
716 if ( seqs != null ) {
\r
717 for( final MolecularSequence seq : seqs ) {
\r
718 System.out.println( seq.getIdentifier() );
\r
720 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
721 int total_counter = 0;
\r
722 int attached_counter = 0;
\r
723 for( final MolecularSequence seq : seqs ) {
\r
725 final String seq_name = seq.getIdentifier();
\r
726 if ( !ForesterUtil.isEmpty( seq_name ) ) {
\r
727 List<PhylogenyNode> nodes = phy.getNodesViaSequenceName( seq_name );
\r
728 if ( nodes.isEmpty() ) {
\r
729 nodes = phy.getNodesViaSequenceSymbol( seq_name );
\r
731 if ( nodes.isEmpty() ) {
\r
732 nodes = phy.getNodesViaGeneName( seq_name );
\r
734 if ( nodes.isEmpty() ) {
\r
735 nodes = phy.getNodes( seq_name );
\r
737 if ( nodes.size() > 1 ) {
\r
738 JOptionPane.showMessageDialog( this,
\r
739 "Sequence name \"" + seq_name + "\" is not unique",
\r
740 "Sequence name not unique",
\r
741 JOptionPane.ERROR_MESSAGE );
\r
745 final String[] a = seq_name.split( "\\s" );
\r
746 if ( nodes.isEmpty() && ( a.length > 1 ) ) {
\r
747 final String seq_name_split = a[ 0 ];
\r
748 nodes = phy.getNodesViaSequenceName( seq_name_split );
\r
749 if ( nodes.isEmpty() ) {
\r
750 nodes = phy.getNodesViaSequenceSymbol( seq_name_split );
\r
752 if ( nodes.isEmpty() ) {
\r
753 nodes = phy.getNodes( seq_name_split );
\r
755 if ( nodes.size() > 1 ) {
\r
756 JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split
\r
757 + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );
\r
762 if ( nodes.size() == 1 ) {
\r
763 ++attached_counter;
\r
764 final PhylogenyNode n = nodes.get( 0 );
\r
765 if ( !n.getNodeData().isHasSequence() ) {
\r
766 n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );
\r
768 n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );
\r
769 if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
\r
770 n.getNodeData().getSequence().setName( seq_name );
\r
775 if ( attached_counter > 0 ) {
\r
777 int ext_nodes_with_seq = 0;
\r
778 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
\r
780 final PhylogenyNode n = iter.next();
\r
781 if ( n.getNodeData().isHasSequence()
\r
782 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
\r
783 ++ext_nodes_with_seq;
\r
787 if ( ext_nodes == ext_nodes_with_seq ) {
\r
788 s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them.";
\r
791 s = ext_nodes_with_seq + " out of " + ext_nodes
\r
792 + " external nodes now have a molecular sequence attached to them.";
\r
794 if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) {
\r
795 JOptionPane.showMessageDialog( this,
\r
796 "Attached all " + total_counter + " sequences to tree nodes.\n" + s,
\r
797 "All sequences attached",
\r
798 JOptionPane.INFORMATION_MESSAGE );
\r
801 JOptionPane.showMessageDialog( this, "Attached " + attached_counter
\r
802 + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter
\r
803 + " sequences attached", JOptionPane.WARNING_MESSAGE );
\r
807 JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter
\r
808 + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );
\r
813 void buildAnalysisMenu() {
\r
814 _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
\r
815 _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
\r
816 _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
\r
817 _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
\r
818 customizeJMenuItem( _gsdi_item );
\r
819 customizeJMenuItem( _gsdir_item );
\r
820 customizeJMenuItem( _load_species_tree_item );
\r
821 _analysis_menu.addSeparator();
\r
822 _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
\r
823 customizeJMenuItem( _lineage_inference );
\r
824 _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
\r
825 _jmenubar.add( _analysis_menu );
\r
829 void buildFileMenu() {
\r
830 _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
\r
831 _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
\r
832 _file_jmenu.addSeparator();
\r
833 _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );
\r
834 _file_jmenu.addSeparator();
\r
835 final WebservicesManager webservices_manager = WebservicesManager.getInstance();
\r
836 _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
\r
837 .getAvailablePhylogeniesWebserviceClients().size() ];
\r
838 for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
\r
839 final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );
\r
840 _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );
\r
841 _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );
\r
843 if ( getConfiguration().isEditable() ) {
\r
844 _file_jmenu.addSeparator();
\r
845 _file_jmenu.add( _new_item = new JMenuItem( "New" ) );
\r
846 _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );
\r
848 _file_jmenu.addSeparator();
\r
849 _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
\r
850 _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );
\r
851 _save_all_item.setToolTipText( "Write all phylogenies to one file." );
\r
852 _save_all_item.setEnabled( false );
\r
853 _file_jmenu.addSeparator();
\r
854 _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
\r
855 if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
\r
856 _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
\r
858 _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
\r
859 _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
\r
860 if ( AptxUtil.canWriteFormat( "gif" ) ) {
\r
861 _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
\r
863 if ( AptxUtil.canWriteFormat( "bmp" ) ) {
\r
864 _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
\r
866 _file_jmenu.addSeparator();
\r
867 _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
\r
868 _file_jmenu.addSeparator();
\r
869 _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );
\r
870 _close_item.setToolTipText( "To close the current pane." );
\r
871 _close_item.setEnabled( true );
\r
872 _file_jmenu.addSeparator();
\r
873 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
\r
874 customizeJMenuItem( _open_item );
\r
876 .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );
\r
877 customizeJMenuItem( _open_url_item );
\r
878 for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
\r
879 customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
\r
881 customizeJMenuItem( _save_item );
\r
882 if ( getConfiguration().isEditable() ) {
\r
883 customizeJMenuItem( _new_item );
\r
885 customizeJMenuItem( _close_item );
\r
886 customizeJMenuItem( _save_all_item );
\r
887 customizeJMenuItem( _write_to_pdf_item );
\r
888 customizeJMenuItem( _write_to_png_item );
\r
889 customizeJMenuItem( _write_to_jpg_item );
\r
890 customizeJMenuItem( _write_to_gif_item );
\r
891 customizeJMenuItem( _write_to_tif_item );
\r
892 customizeJMenuItem( _write_to_bmp_item );
\r
893 customizeJMenuItem( _print_item );
\r
894 customizeJMenuItem( _exit_item );
\r
895 _jmenubar.add( _file_jmenu );
\r
898 void buildOptionsMenu() {
\r
899 _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );
\r
900 _options_jmenu.addChangeListener( new ChangeListener() {
\r
903 public void stateChanged( final ChangeEvent e ) {
\r
904 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
\r
905 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
\r
907 .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
\r
908 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
\r
909 .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
\r
910 MainFrame.setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
\r
911 MainFrame.setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
\r
912 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
\r
913 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
\r
914 MainFrame.setCycleDataReturnMenuItem( _cycle_data_return, getOptions() );
\r
915 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
\r
917 getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
\r
918 getMainPanel().getControlPanel().setVisibilityOfX();
\r
920 catch ( final Exception ignore ) {
\r
921 // do nothing, not important.
\r
925 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
\r
927 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
\r
928 _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
\r
929 _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
\r
930 _radio_group_1 = new ButtonGroup();
\r
931 _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
\r
932 _radio_group_1.add( _uniform_cladograms_rbmi );
\r
933 _radio_group_1.add( _non_lined_up_cladograms_rbmi );
\r
934 _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
\r
935 _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
\r
937 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
\r
939 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
\r
941 .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
\r
942 _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
\r
943 if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
\r
944 _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
\r
945 _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
\r
947 _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );
\r
948 _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
\r
949 _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );
\r
950 _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
\r
951 _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
\r
952 _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
\r
953 _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
\r
954 _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
\r
955 _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
\r
956 _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
\r
957 _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
\r
958 _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
\r
959 _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
\r
960 _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
\r
961 _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
\r
962 _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
\r
963 _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
\r
964 _options_jmenu.addSeparator();
\r
965 _options_jmenu.add( _cycle_data_return = new JMenuItem( "Cycle Data Return" ) );
\r
966 _options_jmenu.addSeparator();
\r
967 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
\r
968 _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
\r
969 _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
\r
970 _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
\r
971 _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );
\r
972 _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
\r
973 _options_jmenu.addSeparator();
\r
974 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
\r
975 getConfiguration() ) );
\r
976 _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
\r
977 _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
\r
979 .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
\r
981 .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
\r
983 .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
\r
984 _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
\r
985 _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
\r
986 _options_jmenu.addSeparator();
\r
987 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );
\r
989 .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
\r
990 _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
\r
992 .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );
\r
993 _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
\r
995 .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );
\r
997 .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );
\r
999 .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );
\r
1000 _extract_taxonomy_pfam_strict_rbmi
\r
1001 .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );
\r
1002 _extract_taxonomy_pfam_relaxed_rbmi
\r
1003 .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );
\r
1004 _extract_taxonomy_agressive_rbmi
\r
1005 .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" );
\r
1006 _radio_group_2 = new ButtonGroup();
\r
1007 _radio_group_2.add( _extract_taxonomy_no_rbmi );
\r
1008 _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );
\r
1009 _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );
\r
1010 _radio_group_2.add( _extract_taxonomy_agressive_rbmi );
\r
1011 _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );
\r
1013 .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
\r
1014 _use_brackets_for_conf_in_nh_export_cbmi
\r
1015 .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
\r
1017 .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
\r
1018 customizeJMenuItem( _choose_font_mi );
\r
1019 customizeJMenuItem( _choose_minimal_confidence_mi );
\r
1020 customizeJMenuItem( _switch_colors_mi );
\r
1021 customizeJMenuItem( _print_size_mi );
\r
1022 customizeJMenuItem( _choose_pdf_width_mi );
\r
1023 customizeJMenuItem( _overview_placment_mi );
\r
1024 customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
\r
1025 .isShowDefaultNodeShapesExternal() );
\r
1026 customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
\r
1027 .isShowDefaultNodeShapesInternal() );
\r
1028 customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
\r
1029 .isShowDefaultNodeShapesForMarkedNodes() );
\r
1030 customizeJMenuItem( _cycle_node_shape_mi );
\r
1031 customizeJMenuItem( _cycle_node_fill_mi );
\r
1032 customizeJMenuItem( _choose_node_size_mi );
\r
1033 customizeJMenuItem( _cycle_data_return );
\r
1034 customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
\r
1035 customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
\r
1036 customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
\r
1037 customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
\r
1038 customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
\r
1039 customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
\r
1040 customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
\r
1041 customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
\r
1042 customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
\r
1043 customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
\r
1044 getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
\r
1045 customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
\r
1046 getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
\r
1047 customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
\r
1048 getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
\r
1049 customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
\r
1050 customizeCheckBoxMenuItem( _label_direction_cbmi,
\r
1051 getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
\r
1052 customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
\r
1053 customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
\r
1054 customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
\r
1055 .isInternalNumberAreConfidenceForNhParsing() );
\r
1056 customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
\r
1057 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
\r
1058 customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,
\r
1059 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
\r
1060 customizeRadioButtonMenuItem( _extract_taxonomy_pfam_relaxed_rbmi,
\r
1061 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
\r
1062 customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,
\r
1063 getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );
\r
1064 customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
\r
1065 customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions()
\r
1066 .isReplaceUnderscoresInNhParsing() );
\r
1067 customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );
\r
1068 customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
\r
1069 customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
\r
1070 customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
\r
1071 customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
\r
1072 customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
\r
1073 .isGraphicsExportUsingActualSize() );
\r
1074 customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
\r
1075 customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
\r
1076 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
\r
1077 customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
\r
1078 .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
\r
1079 customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
\r
1080 customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
\r
1081 _jmenubar.add( _options_jmenu );
\r
1084 void buildPhylogeneticInferenceMenu() {
\r
1085 final InferenceManager im = getInferenceManager();
\r
1086 _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
\r
1087 _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
\r
1088 customizeJMenuItem( _inference_from_msa_item );
\r
1089 _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
\r
1090 if ( im.canDoMsa() ) {
\r
1091 _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
\r
1092 customizeJMenuItem( _inference_from_seqs_item );
\r
1093 _inference_from_seqs_item
\r
1094 .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
\r
1098 .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
\r
1099 customizeJMenuItem( _inference_from_seqs_item );
\r
1100 _inference_from_seqs_item.setEnabled( false );
\r
1102 _jmenubar.add( _inference_menu );
\r
1105 void buildToolsMenu() {
\r
1106 _tools_menu = createMenu( "Tools", getConfiguration() );
\r
1107 _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
\r
1108 customizeJMenuItem( _confcolor_item );
\r
1109 _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );
\r
1110 customizeJMenuItem( _color_rank_jmi );
\r
1111 _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
\r
1112 _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
\r
1113 customizeJMenuItem( _taxcolor_item );
\r
1114 _tools_menu.addSeparator();
\r
1115 _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
\r
1116 _remove_visual_styles_item
\r
1117 .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny" );
\r
1118 customizeJMenuItem( _remove_visual_styles_item );
\r
1119 _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
\r
1120 _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny" );
\r
1121 customizeJMenuItem( _remove_branch_color_item );
\r
1122 _tools_menu.addSeparator();
\r
1123 _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );
\r
1124 customizeJMenuItem( _annotate_item );
\r
1125 _tools_menu.addSeparator();
\r
1126 _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
\r
1127 customizeJMenuItem( _midpoint_root_item );
\r
1128 _tools_menu.addSeparator();
\r
1129 _tools_menu.add( _delete_selected_nodes_item = new JMenuItem( "Delete Selected Nodes" ) );
\r
1130 _delete_selected_nodes_item.setToolTipText( "To delete all selected external nodes" );
\r
1131 customizeJMenuItem( _delete_selected_nodes_item );
\r
1132 _tools_menu.add( _delete_not_selected_nodes_item = new JMenuItem( "Retain Selected Nodes" ) );
\r
1133 _delete_not_selected_nodes_item.setToolTipText( "To delete all not selected external nodes" );
\r
1134 customizeJMenuItem( _delete_not_selected_nodes_item );
\r
1135 _tools_menu.addSeparator();
\r
1136 _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
\r
1137 customizeJMenuItem( _collapse_species_specific_subtrees );
\r
1138 _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse species-specific subtrees" );
\r
1140 .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
\r
1141 customizeJMenuItem( _collapse_below_threshold );
\r
1142 _collapse_below_threshold
\r
1143 .setToolTipText( "To (permanently) collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" );
\r
1146 .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) );
\r
1147 customizeJMenuItem( _collapse_below_branch_length );
\r
1148 _collapse_below_branch_length
\r
1149 .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" );
\r
1151 _tools_menu.addSeparator();
\r
1153 .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );
\r
1154 customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
\r
1155 _extract_tax_code_from_node_names_jmi
\r
1156 .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );
\r
1158 .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
\r
1159 customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
\r
1160 _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
\r
1161 _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
\r
1162 customizeJMenuItem( _move_node_names_to_seq_names_jmi );
\r
1163 _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
\r
1164 _tools_menu.addSeparator();
\r
1165 _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
\r
1166 customizeJMenuItem( _obtain_seq_information_jmi );
\r
1167 _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
\r
1169 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
\r
1170 customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
\r
1171 _obtain_detailed_taxonomic_information_jmi
\r
1172 .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
\r
1174 .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
\r
1175 customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
\r
1176 _obtain_detailed_taxonomic_information_deleting_jmi
\r
1177 .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
\r
1178 _tools_menu.addSeparator();
\r
1179 _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );
\r
1180 customizeJMenuItem( _read_values_jmi );
\r
1181 _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );
\r
1182 _jmenubar.add( _tools_menu );
\r
1183 _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );
\r
1184 customizeJMenuItem( _read_seqs_jmi );
\r
1186 .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );
\r
1187 _jmenubar.add( _tools_menu );
\r
1192 if ( isUnsavedDataPresent() ) {
\r
1193 final int r = JOptionPane.showConfirmDialog( this,
\r
1194 "Exit despite potentially unsaved changes?",
\r
1196 JOptionPane.YES_NO_OPTION );
\r
1197 if ( r != JOptionPane.YES_OPTION ) {
\r
1204 private void closeCurrentPane() {
\r
1205 if ( getMainPanel().getCurrentTreePanel() != null ) {
\r
1206 if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
\r
1207 final int r = JOptionPane.showConfirmDialog( this,
\r
1208 "Close tab despite potentially unsaved changes?",
\r
1210 JOptionPane.YES_NO_OPTION );
\r
1211 if ( r != JOptionPane.YES_OPTION ) {
\r
1215 getMainPanel().closeCurrentPane();
\r
1216 activateSaveAllIfNeeded();
\r
1220 private void collapse( final Phylogeny phy ) {
\r
1221 final PhylogenyNodeIterator it = phy.iteratorPostorder();
\r
1222 final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
\r
1223 double min_support = Double.MAX_VALUE;
\r
1224 boolean conf_present = false;
\r
1225 while ( it.hasNext() ) {
\r
1226 final PhylogenyNode n = it.next();
\r
1227 if ( !n.isExternal() && !n.isRoot() ) {
\r
1228 final List<Confidence> c = n.getBranchData().getConfidences();
\r
1229 if ( ( c != null ) && ( c.size() > 0 ) ) {
\r
1230 conf_present = true;
\r
1232 for( final Confidence confidence : c ) {
\r
1233 if ( confidence.getValue() > max ) {
\r
1234 max = confidence.getValue();
\r
1237 if ( max < getMinNotCollapseConfidenceValue() ) {
\r
1238 to_be_removed.add( n );
\r
1240 if ( max < min_support ) {
\r
1241 min_support = max;
\r
1246 if ( conf_present ) {
\r
1247 for( final PhylogenyNode node : to_be_removed ) {
\r
1248 PhylogenyMethods.removeNode( node, phy );
\r
1250 if ( to_be_removed.size() > 0 ) {
\r
1251 phy.externalNodesHaveChanged();
\r
1252 phy.clearHashIdToNodeMap();
\r
1253 phy.recalculateNumberOfExternalDescendants( true );
\r
1254 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
\r
1255 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
\r
1256 getCurrentTreePanel().calculateLongestExtNodeInfo();
\r
1257 getCurrentTreePanel().setNodeInPreorderToNull();
\r
1258 getCurrentTreePanel().recalculateMaxDistanceToRoot();
\r
1259 getCurrentTreePanel().resetPreferredSize();
\r
1260 getCurrentTreePanel().setEdited( true );
\r
1261 getCurrentTreePanel().repaint();
\r
1264 if ( to_be_removed.size() > 0 ) {
\r
1265 JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
\r
1266 + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "
\r
1267 + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
\r
1270 JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "
\r
1271 + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );
\r
1275 JOptionPane.showMessageDialog( this,
\r
1276 "No branch collapsed because no confidence values present",
\r
1277 "No confidence values present",
\r
1278 JOptionPane.INFORMATION_MESSAGE );
\r
1282 private void collapseBelowBranchLengthThreshold() {
\r
1283 if ( getCurrentTreePanel() != null ) {
\r
1284 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1285 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1286 final String s = ( String ) JOptionPane
\r
1287 .showInputDialog( this,
\r
1288 "Please enter the minimum branch length value\n",
\r
1289 "Minimal Branch Length Value",
\r
1290 JOptionPane.QUESTION_MESSAGE,
\r
1293 getMinNotCollapseBlValue() );
\r
1294 if ( !ForesterUtil.isEmpty( s ) ) {
\r
1295 boolean success = true;
\r
1297 final String m_str = s.trim();
\r
1298 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
1300 m = Double.parseDouble( m_str );
\r
1302 catch ( final Exception ex ) {
\r
1309 if ( success && ( m >= 0.0 ) ) {
\r
1310 setMinNotCollapseBlValue( m );
\r
1311 collapseBl( phy );
\r
1318 private void collapseBelowThreshold() {
\r
1319 if ( getCurrentTreePanel() != null ) {
\r
1320 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1321 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1322 final String s = ( String ) JOptionPane.showInputDialog( this,
\r
1323 "Please enter the minimum confidence value\n",
\r
1324 "Minimal Confidence Value",
\r
1325 JOptionPane.QUESTION_MESSAGE,
\r
1328 getMinNotCollapseConfidenceValue() );
\r
1329 if ( !ForesterUtil.isEmpty( s ) ) {
\r
1330 boolean success = true;
\r
1332 final String m_str = s.trim();
\r
1333 if ( !ForesterUtil.isEmpty( m_str ) ) {
\r
1335 m = Double.parseDouble( m_str );
\r
1337 catch ( final Exception ex ) {
\r
1344 if ( success && ( m >= 0.0 ) ) {
\r
1345 setMinNotCollapseConfidenceValue( m );
\r
1353 private void collapseBl( final Phylogeny phy ) {
\r
1354 final PhylogenyNodeIterator it = phy.iteratorPostorder();
\r
1355 final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
\r
1356 double min_bl = Double.MAX_VALUE;
\r
1357 boolean bl_present = false;
\r
1358 while ( it.hasNext() ) {
\r
1359 final PhylogenyNode n = it.next();
\r
1360 if ( !n.isExternal() && !n.isRoot() ) {
\r
1361 final double bl = n.getDistanceToParent();
\r
1362 if ( bl != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
\r
1363 bl_present = true;
\r
1364 if ( bl < getMinNotCollapseBlValue() ) {
\r
1365 to_be_removed.add( n );
\r
1367 if ( bl < min_bl ) {
\r
1373 if ( bl_present ) {
\r
1374 for( final PhylogenyNode node : to_be_removed ) {
\r
1375 PhylogenyMethods.removeNode( node, phy );
\r
1377 if ( to_be_removed.size() > 0 ) {
\r
1378 phy.externalNodesHaveChanged();
\r
1379 phy.clearHashIdToNodeMap();
\r
1380 phy.recalculateNumberOfExternalDescendants( true );
\r
1381 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
\r
1382 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
\r
1383 getCurrentTreePanel().calculateLongestExtNodeInfo();
\r
1384 getCurrentTreePanel().setNodeInPreorderToNull();
\r
1385 getCurrentTreePanel().recalculateMaxDistanceToRoot();
\r
1386 getCurrentTreePanel().resetPreferredSize();
\r
1387 getCurrentTreePanel().setEdited( true );
\r
1388 getCurrentTreePanel().repaint();
\r
1391 if ( to_be_removed.size() > 0 ) {
\r
1392 JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
\r
1393 + " branches with\nbranch length values below " + getMinNotCollapseBlValue(), "Collapsed "
\r
1394 + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
\r
1397 JOptionPane.showMessageDialog( this,
\r
1398 "No branch collapsed,\nminimum branch length is " + min_bl,
\r
1399 "No branch collapsed",
\r
1400 JOptionPane.INFORMATION_MESSAGE );
\r
1404 JOptionPane.showMessageDialog( this,
\r
1405 "No branch collapsed because no branch length values present",
\r
1406 "No branch length values present",
\r
1407 JOptionPane.INFORMATION_MESSAGE );
\r
1411 private PhyloXmlParser createPhyloXmlParser() {
\r
1412 PhyloXmlParser xml_parser = null;
\r
1413 if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
\r
1415 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
\r
1417 catch ( final Exception e ) {
\r
1418 JOptionPane.showMessageDialog( this,
\r
1419 e.getLocalizedMessage(),
\r
1420 "failed to create validating XML parser",
\r
1421 JOptionPane.WARNING_MESSAGE );
\r
1424 if ( xml_parser == null ) {
\r
1425 xml_parser = PhyloXmlParser.createPhyloXmlParser();
\r
1427 return xml_parser;
\r
1430 public void end() {
\r
1431 _mainpanel.terminate();
\r
1432 _contentpane.removeAll();
\r
1433 setVisible( false );
\r
1437 void executeLineageInference() {
\r
1438 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
\r
1441 if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
\r
1442 JOptionPane.showMessageDialog( this,
\r
1443 "Phylogeny is not rooted.",
\r
1444 "Cannot infer ancestral taxonomies",
\r
1445 JOptionPane.ERROR_MESSAGE );
\r
1448 final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
\r
1449 _mainpanel.getCurrentTreePanel(),
\r
1450 _mainpanel.getCurrentPhylogeny()
\r
1452 new Thread( inferrer ).start();
\r
1455 private void executePhyleneticInference( final boolean from_unaligned_seqs ) {
\r
1456 final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,
\r
1457 getPhylogeneticInferenceOptions(),
\r
1458 from_unaligned_seqs );
\r
1459 dialog.activate();
\r
1460 if ( dialog.getValue() == JOptionPane.OK_OPTION ) {
\r
1461 if ( !from_unaligned_seqs ) {
\r
1462 if ( getMsa() != null ) {
\r
1463 final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
\r
1464 getPhylogeneticInferenceOptions()
\r
1466 new Thread( inferrer ).start();
\r
1469 JOptionPane.showMessageDialog( this,
\r
1470 "No multiple sequence alignment selected",
\r
1471 "Phylogenetic Inference Not Launched",
\r
1472 JOptionPane.WARNING_MESSAGE );
\r
1476 if ( getSeqs() != null ) {
\r
1477 final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
\r
1478 getPhylogeneticInferenceOptions()
\r
1480 new Thread( inferrer ).start();
\r
1483 JOptionPane.showMessageDialog( this,
\r
1484 "No input sequences selected",
\r
1485 "Phylogenetic Inference Not Launched",
\r
1486 JOptionPane.WARNING_MESSAGE );
\r
1493 removeAllTextFrames();
\r
1494 _mainpanel.terminate();
\r
1495 _contentpane.removeAll();
\r
1496 setVisible( false );
\r
1498 // System.exit( 0 ); //TODO reconfirm that this is OK, then remove.
\r
1501 private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {
\r
1502 final StringBuilder sb = new StringBuilder();
\r
1503 final StringBuilder sb_failed = new StringBuilder();
\r
1505 int counter_failed = 0;
\r
1506 if ( getCurrentTreePanel() != null ) {
\r
1507 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1508 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1509 final PhylogenyNodeIterator it = phy.iteratorExternalForward();
\r
1510 while ( it.hasNext() ) {
\r
1511 final PhylogenyNode n = it.next();
\r
1512 final String name = n.getName().trim();
\r
1513 if ( !ForesterUtil.isEmpty( name ) ) {
\r
1514 final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n,
\r
1515 TAXONOMY_EXTRACTION.AGGRESSIVE );
\r
1516 if ( !ForesterUtil.isEmpty( nt ) ) {
\r
1517 if ( counter < 15 ) {
\r
1518 sb.append( name + ": " + nt + "\n" );
\r
1520 else if ( counter == 15 ) {
\r
1521 sb.append( "...\n" );
\r
1526 if ( counter_failed < 15 ) {
\r
1527 sb_failed.append( name + "\n" );
\r
1529 else if ( counter_failed == 15 ) {
\r
1530 sb_failed.append( "...\n" );
\r
1536 if ( counter > 0 ) {
\r
1537 String failed = "";
\r
1538 String all = "all ";
\r
1539 if ( counter_failed > 0 ) {
\r
1541 failed = "\nCould not extract taxonomic data for " + counter_failed
\r
1542 + " named external nodes:\n" + sb_failed;
\r
1544 JOptionPane.showMessageDialog( this,
\r
1545 "Extracted taxonomic data from " + all + counter
\r
1546 + " named external nodes:\n" + sb.toString() + failed,
\r
1547 "Taxonomic Data Extraction Completed",
\r
1548 counter_failed > 0 ? JOptionPane.WARNING_MESSAGE
\r
1549 : JOptionPane.INFORMATION_MESSAGE );
\r
1553 .showMessageDialog( this,
\r
1554 "Could not extract any taxonomic data.\nMaybe node names are empty\n"
\r
1555 + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
\r
1556 + "or nodes already have taxonomic data?\n",
\r
1557 "No Taxonomic Data Extracted",
\r
1558 JOptionPane.ERROR_MESSAGE );
\r
1565 public MainPanel getMainPanel() {
\r
1566 return _mainpanel;
\r
1569 private double getMinNotCollapseBlValue() {
\r
1570 return _min_not_collapse_bl;
\r
1573 private double getMinNotCollapseConfidenceValue() {
\r
1574 return _min_not_collapse;
\r
1577 public Msa getMsa() {
\r
1581 public File getMsaFile() {
\r
1585 private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
\r
1586 if ( _phylogenetic_inference_options == null ) {
\r
1587 _phylogenetic_inference_options = new PhylogeneticInferenceOptions();
\r
1589 return _phylogenetic_inference_options;
\r
1592 public List<MolecularSequence> getSeqs() {
\r
1596 public File getSeqsFile() {
\r
1597 return _seqs_file;
\r
1600 private boolean isUnsavedDataPresent() {
\r
1601 final List<TreePanel> tps = getMainPanel().getTreePanels();
\r
1602 for( final TreePanel tp : tps ) {
\r
1603 if ( tp.isEdited() ) {
\r
1610 private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
\r
1611 if ( getCurrentTreePanel() != null ) {
\r
1612 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1613 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1615 .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );
\r
1620 private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
\r
1621 if ( getCurrentTreePanel() != null ) {
\r
1622 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1623 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1624 PhylogenyMethods.transferNodeNameToField( phy,
\r
1625 PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
\r
1631 private void newTree() {
\r
1632 final Phylogeny[] phys = new Phylogeny[ 1 ];
\r
1633 final Phylogeny phy = new Phylogeny();
\r
1634 final PhylogenyNode node = new PhylogenyNode();
\r
1635 phy.setRoot( node );
\r
1636 phy.setRooted( true );
\r
1638 AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
\r
1639 _mainpanel.getControlPanel().showWhole();
\r
1640 _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
1641 _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
1642 if ( getMainPanel().getMainFrame() == null ) {
\r
1643 // Must be "E" applet version.
\r
1644 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
\r
1645 .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
1648 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
\r
1650 activateSaveAllIfNeeded();
\r
1654 private void obtainDetailedTaxonomicInformation() {
\r
1655 if ( getCurrentTreePanel() != null ) {
\r
1656 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1657 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1658 final TaxonomyDataManager t = new TaxonomyDataManager( this,
\r
1659 _mainpanel.getCurrentTreePanel(),
\r
1663 new Thread( t ).start();
\r
1668 private void obtainDetailedTaxonomicInformationDelete() {
\r
1669 if ( getCurrentTreePanel() != null ) {
\r
1670 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1671 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1672 final TaxonomyDataManager t = new TaxonomyDataManager( this,
\r
1673 _mainpanel.getCurrentTreePanel(),
\r
1677 new Thread( t ).start();
\r
1682 private void obtainSequenceInformation() {
\r
1683 if ( getCurrentTreePanel() != null ) {
\r
1684 final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
\r
1685 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1686 final SequenceDataRetriver u = new SequenceDataRetriver( this,
\r
1687 _mainpanel.getCurrentTreePanel(),
\r
1689 new Thread( u ).start();
\r
1694 private void preProcessTreesUponReading( final Phylogeny[] phys ) {
\r
1695 for( final Phylogeny phy : phys ) {
\r
1696 if ( ( phy != null ) && !phy.isEmpty() ) {
\r
1697 for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
\r
1698 final PhylogenyNode n = it.next();
\r
1699 if ( n.isExternal() ) {
\r
1700 if ( n.getNodeData().isHasSequence() ) {
\r
1701 final Sequence s = n.getNodeData().getSequence();
\r
1702 if ( ForesterUtil.isEmpty( s.getGeneName() ) || s.getGeneName().startsWith( "LOC" ) ) {
\r
1703 if ( ( s.getAccession() != null )
\r
1704 && !ForesterUtil.isEmpty( s.getAccession().getValue() ) ) {
\r
1705 s.setGeneName( s.getAccession().getValue() );
\r
1707 else if ( !ForesterUtil.isEmpty( n.getName() ) ) {
\r
1708 s.setGeneName( n.getName() );
\r
1720 public void readMsaFromFile() {
\r
1721 // Set an initial directory if none set yet
\r
1722 final File my_dir = getCurrentDir();
\r
1723 _msa_filechooser.setMultiSelectionEnabled( false );
\r
1724 // Open file-open dialog and set current directory
\r
1725 if ( my_dir != null ) {
\r
1726 _msa_filechooser.setCurrentDirectory( my_dir );
\r
1728 final int result = _msa_filechooser.showOpenDialog( _contentpane );
\r
1729 // All done: get the msa
\r
1730 final File file = _msa_filechooser.getSelectedFile();
\r
1731 setCurrentDir( _msa_filechooser.getCurrentDirectory() );
\r
1732 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
1733 setMsaFile( null );
\r
1737 final InputStream is = new FileInputStream( file );
\r
1738 if ( FastaParser.isLikelyFasta( file ) ) {
\r
1739 msa = FastaParser.parseMsa( is );
\r
1742 msa = GeneralMsaParser.parse( is );
\r
1745 catch ( final MsaFormatException e ) {
\r
1747 JOptionPane.showMessageDialog( this,
\r
1748 e.getLocalizedMessage(),
\r
1749 "Multiple sequence alignment format error",
\r
1750 JOptionPane.ERROR_MESSAGE );
\r
1753 catch ( final IOException e ) {
\r
1755 JOptionPane.showMessageDialog( this,
\r
1756 e.getLocalizedMessage(),
\r
1757 "Failed to read multiple sequence alignment",
\r
1758 JOptionPane.ERROR_MESSAGE );
\r
1761 catch ( final IllegalArgumentException e ) {
\r
1763 JOptionPane.showMessageDialog( this,
\r
1764 e.getLocalizedMessage(),
\r
1765 "Unexpected error during reading of multiple sequence alignment",
\r
1766 JOptionPane.ERROR_MESSAGE );
\r
1769 catch ( final Exception e ) {
\r
1771 e.printStackTrace();
\r
1772 JOptionPane.showMessageDialog( this,
\r
1773 e.getLocalizedMessage(),
\r
1774 "Unexpected error during reading of multiple sequence alignment",
\r
1775 JOptionPane.ERROR_MESSAGE );
\r
1778 if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {
\r
1779 JOptionPane.showMessageDialog( this,
\r
1780 "Multiple sequence alignment is empty",
\r
1781 "Illegal Multiple Sequence Alignment",
\r
1782 JOptionPane.ERROR_MESSAGE );
\r
1785 if ( msa.getNumberOfSequences() < 4 ) {
\r
1786 JOptionPane.showMessageDialog( this,
\r
1787 "Multiple sequence alignment needs to contain at least 3 sequences",
\r
1788 "Illegal multiple sequence alignment",
\r
1789 JOptionPane.ERROR_MESSAGE );
\r
1792 if ( msa.getLength() < 2 ) {
\r
1793 JOptionPane.showMessageDialog( this,
\r
1794 "Multiple sequence alignment needs to contain at least 2 residues",
\r
1795 "Illegal multiple sequence alignment",
\r
1796 JOptionPane.ERROR_MESSAGE );
\r
1800 setMsaFile( _msa_filechooser.getSelectedFile() );
\r
1805 private void readPhylogeniesFromFile() {
\r
1806 boolean exception = false;
\r
1807 Phylogeny[] phys = null;
\r
1808 // Set an initial directory if none set yet
\r
1809 final File my_dir = getCurrentDir();
\r
1810 _open_filechooser.setMultiSelectionEnabled( true );
\r
1811 // Open file-open dialog and set current directory
\r
1812 if ( my_dir != null ) {
\r
1813 _open_filechooser.setCurrentDirectory( my_dir );
\r
1815 final int result = _open_filechooser.showOpenDialog( _contentpane );
\r
1816 // All done: get the file
\r
1817 final File[] files = _open_filechooser.getSelectedFiles();
\r
1818 setCurrentDir( _open_filechooser.getCurrentDirectory() );
\r
1819 boolean nhx_or_nexus = false;
\r
1820 if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
1821 for( final File file : files ) {
\r
1822 if ( ( file != null ) && !file.isDirectory() ) {
\r
1823 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1824 _mainpanel.getCurrentTreePanel().setWaitCursor();
\r
1827 _mainpanel.setWaitCursor();
\r
1829 if ( ( _open_filechooser.getFileFilter() == MainFrame.nhfilter )
\r
1830 || ( _open_filechooser.getFileFilter() == MainFrame.nhxfilter ) ) {
\r
1832 final NHXParser nhx = new NHXParser();
\r
1833 setSpecialOptionsForNhxParser( nhx );
\r
1834 phys = PhylogenyMethods.readPhylogenies( nhx, file );
\r
1835 nhx_or_nexus = true;
\r
1837 catch ( final Exception e ) {
\r
1839 exceptionOccuredDuringOpenFile( e );
\r
1842 else if ( _open_filechooser.getFileFilter() == MainFrame.xmlfilter ) {
\r
1843 warnIfNotPhyloXmlValidation( getConfiguration() );
\r
1845 final PhyloXmlParser xml_parser = createPhyloXmlParser();
\r
1846 phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
\r
1848 catch ( final Exception e ) {
\r
1850 exceptionOccuredDuringOpenFile( e );
\r
1853 else if ( _open_filechooser.getFileFilter() == MainFrame.tolfilter ) {
\r
1855 phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
\r
1857 catch ( final Exception e ) {
\r
1859 exceptionOccuredDuringOpenFile( e );
\r
1862 else if ( _open_filechooser.getFileFilter() == MainFrame.nexusfilter ) {
\r
1864 final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
\r
1865 setSpecialOptionsForNexParser( nex );
\r
1866 phys = PhylogenyMethods.readPhylogenies( nex, file );
\r
1867 nhx_or_nexus = true;
\r
1869 catch ( final Exception e ) {
\r
1871 exceptionOccuredDuringOpenFile( e );
\r
1877 final PhylogenyParser parser = ParserUtils
\r
1878 .createParserDependingOnFileType( file, getConfiguration()
\r
1879 .isValidatePhyloXmlAgainstSchema() );
\r
1880 if ( parser instanceof NexusPhylogeniesParser ) {
\r
1881 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
\r
1882 setSpecialOptionsForNexParser( nex );
\r
1883 nhx_or_nexus = true;
\r
1885 else if ( parser instanceof NHXParser ) {
\r
1886 final NHXParser nhx = ( NHXParser ) parser;
\r
1887 setSpecialOptionsForNhxParser( nhx );
\r
1888 nhx_or_nexus = true;
\r
1890 else if ( parser instanceof PhyloXmlParser ) {
\r
1891 warnIfNotPhyloXmlValidation( getConfiguration() );
\r
1893 phys = PhylogenyMethods.readPhylogenies( parser, file );
\r
1895 catch ( final Exception e ) {
\r
1897 exceptionOccuredDuringOpenFile( e );
\r
1900 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1901 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
1904 _mainpanel.setArrowCursor();
\r
1906 if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {
\r
1907 boolean one_desc = false;
\r
1908 if ( nhx_or_nexus ) {
\r
1909 for( final Phylogeny phy : phys ) {
\r
1910 if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
\r
1911 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
\r
1913 if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
\r
1919 if ( PREPROCESS_TREES ) {
\r
1920 preProcessTreesUponReading( phys );
\r
1922 AptxUtil.addPhylogeniesToTabs( phys,
\r
1924 file.getAbsolutePath(),
\r
1925 getConfiguration(),
\r
1927 _mainpanel.getControlPanel().showWhole();
\r
1928 if ( nhx_or_nexus && one_desc ) {
\r
1930 .showMessageDialog( this,
\r
1931 "One or more trees contain (a) node(s) with one descendant, "
\r
1932 + ForesterUtil.LINE_SEPARATOR
\r
1933 + "possibly indicating illegal parentheses within node names.",
\r
1934 "Warning: Possible Error in New Hampshire Formatted Data",
\r
1935 JOptionPane.WARNING_MESSAGE );
\r
1941 activateSaveAllIfNeeded();
\r
1945 void readPhylogeniesFromURL() {
\r
1947 Phylogeny[] phys = null;
\r
1948 final String message = "Please enter a complete URL, for example \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"";
\r
1949 final String url_string = JOptionPane.showInputDialog( this,
\r
1951 "Use URL/webservice to obtain a phylogeny",
\r
1952 JOptionPane.QUESTION_MESSAGE );
\r
1953 boolean nhx_or_nexus = false;
\r
1954 if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
\r
1956 url = new URL( url_string );
\r
1957 PhylogenyParser parser = null;
\r
1958 if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
\r
1959 parser = new TolParser();
\r
1962 parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
\r
1963 .isValidatePhyloXmlAgainstSchema() );
\r
1965 if ( parser instanceof NexusPhylogeniesParser ) {
\r
1966 nhx_or_nexus = true;
\r
1968 else if ( parser instanceof NHXParser ) {
\r
1969 nhx_or_nexus = true;
\r
1971 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
1972 _mainpanel.getCurrentTreePanel().setWaitCursor();
\r
1975 _mainpanel.setWaitCursor();
\r
1977 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
\r
1978 phys = factory.create( url.openStream(), parser );
\r
1980 catch ( final MalformedURLException e ) {
\r
1981 JOptionPane.showMessageDialog( this,
\r
1982 "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
\r
1984 JOptionPane.ERROR_MESSAGE );
\r
1986 catch ( final IOException e ) {
\r
1987 JOptionPane.showMessageDialog( this,
\r
1988 "Could not read from " + url + "\n"
\r
1989 + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
\r
1990 "Failed to read URL",
\r
1991 JOptionPane.ERROR_MESSAGE );
\r
1993 catch ( final Exception e ) {
\r
1994 JOptionPane.showMessageDialog( this,
\r
1995 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
\r
1996 "Unexpected Exception",
\r
1997 JOptionPane.ERROR_MESSAGE );
\r
2000 if ( _mainpanel.getCurrentTreePanel() != null ) {
\r
2001 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
2004 _mainpanel.setArrowCursor();
\r
2007 if ( ( phys != null ) && ( phys.length > 0 ) ) {
\r
2008 if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
\r
2009 for( final Phylogeny phy : phys ) {
\r
2010 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
\r
2013 AptxUtil.addPhylogeniesToTabs( phys,
\r
2014 new File( url.getFile() ).getName(),
\r
2015 new File( url.getFile() ).toString(),
\r
2016 getConfiguration(),
\r
2018 _mainpanel.getControlPanel().showWhole();
\r
2021 activateSaveAllIfNeeded();
\r
2025 public void readSeqsFromFileforPI() {
\r
2026 // Set an initial directory if none set yet
\r
2027 final File my_dir = getCurrentDir();
\r
2028 _seqs_pi_filechooser.setMultiSelectionEnabled( false );
\r
2029 // Open file-open dialog and set current directory
\r
2030 if ( my_dir != null ) {
\r
2031 _seqs_pi_filechooser.setCurrentDirectory( my_dir );
\r
2033 final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );
\r
2034 // All done: get the seqs
\r
2035 final File file = _seqs_pi_filechooser.getSelectedFile();
\r
2036 setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );
\r
2037 if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2038 setSeqsFile( null );
\r
2040 List<MolecularSequence> seqs = null;
\r
2042 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
\r
2043 seqs = FastaParser.parse( new FileInputStream( file ) );
\r
2044 for( final MolecularSequence seq : seqs ) {
\r
2045 System.out.println( SequenceWriter.toFasta( seq, 60 ) );
\r
2052 catch ( final MsaFormatException e ) {
\r
2054 JOptionPane.showMessageDialog( this,
\r
2055 e.getLocalizedMessage(),
\r
2056 "Multiple sequence file format error",
\r
2057 JOptionPane.ERROR_MESSAGE );
\r
2060 catch ( final IOException e ) {
\r
2062 JOptionPane.showMessageDialog( this,
\r
2063 e.getLocalizedMessage(),
\r
2064 "Failed to read multiple sequence file",
\r
2065 JOptionPane.ERROR_MESSAGE );
\r
2068 catch ( final IllegalArgumentException e ) {
\r
2070 JOptionPane.showMessageDialog( this,
\r
2071 e.getLocalizedMessage(),
\r
2072 "Unexpected error during reading of multiple sequence file",
\r
2073 JOptionPane.ERROR_MESSAGE );
\r
2076 catch ( final Exception e ) {
\r
2078 e.printStackTrace();
\r
2079 JOptionPane.showMessageDialog( this,
\r
2080 e.getLocalizedMessage(),
\r
2081 "Unexpected error during reading of multiple sequence file",
\r
2082 JOptionPane.ERROR_MESSAGE );
\r
2085 if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
\r
2086 JOptionPane.showMessageDialog( this,
\r
2087 "Multiple sequence file is empty",
\r
2088 "Illegal multiple sequence file",
\r
2089 JOptionPane.ERROR_MESSAGE );
\r
2092 if ( seqs.size() < 4 ) {
\r
2093 JOptionPane.showMessageDialog( this,
\r
2094 "Multiple sequence file needs to contain at least 3 sequences",
\r
2095 "Illegal multiple sequence file",
\r
2096 JOptionPane.ERROR_MESSAGE );
\r
2099 // if ( msa.getLength() < 2 ) {
\r
2100 // JOptionPane.showMessageDialog( this,
\r
2101 // "Multiple sequence alignment needs to contain at least 2 residues",
\r
2102 // "Illegal multiple sequence file",
\r
2103 // JOptionPane.ERROR_MESSAGE );
\r
2107 setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );
\r
2112 private void readSpeciesTreeFromFile() {
\r
2113 Phylogeny t = null;
\r
2114 boolean exception = false;
\r
2115 final File my_dir = getCurrentDir();
\r
2116 _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );
\r
2117 if ( my_dir != null ) {
\r
2118 _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );
\r
2120 final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );
\r
2121 final File file = _open_filechooser_for_species_tree.getSelectedFile();
\r
2122 if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
\r
2123 if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.xmlfilter ) {
\r
2125 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
\r
2126 .createPhyloXmlParserXsdValidating(), file );
\r
2129 catch ( final Exception e ) {
\r
2131 exceptionOccuredDuringOpenFile( e );
\r
2134 else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.tolfilter ) {
\r
2136 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
\r
2139 catch ( final Exception e ) {
\r
2141 exceptionOccuredDuringOpenFile( e );
\r
2147 final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
\r
2148 .createPhyloXmlParserXsdValidating(), file );
\r
2151 catch ( final Exception e ) {
\r
2153 exceptionOccuredDuringOpenFile( e );
\r
2156 if ( !exception && ( t != null ) && !t.isRooted() ) {
\r
2159 JOptionPane.showMessageDialog( this,
\r
2160 "Species tree is not rooted",
\r
2161 "Species tree not loaded",
\r
2162 JOptionPane.ERROR_MESSAGE );
\r
2164 if ( !exception && ( t != null ) ) {
\r
2165 final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
\r
2166 for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {
\r
2167 final PhylogenyNode node = it.next();
\r
2168 if ( !node.getNodeData().isHasTaxonomy() ) {
\r
2172 .showMessageDialog( this,
\r
2173 "Species tree contains external node(s) without taxonomy information",
\r
2174 "Species tree not loaded",
\r
2175 JOptionPane.ERROR_MESSAGE );
\r
2179 if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
\r
2182 JOptionPane.showMessageDialog( this,
\r
2184 + node.getNodeData().getTaxonomy().asSimpleText()
\r
2185 + "] is not unique in species tree",
\r
2186 "Species tree not loaded",
\r
2187 JOptionPane.ERROR_MESSAGE );
\r
2191 tax_set.add( node.getNodeData().getTaxonomy() );
\r
2196 if ( !exception && ( t != null ) ) {
\r
2197 setSpeciesTree( t );
\r
2198 JOptionPane.showMessageDialog( this,
\r
2199 "Species tree successfully loaded",
\r
2200 "Species tree loaded",
\r
2201 JOptionPane.INFORMATION_MESSAGE );
\r
2203 _contentpane.repaint();
\r
2208 private void setArrowCursor() {
\r
2210 _mainpanel.getCurrentTreePanel().setArrowCursor();
\r
2212 catch ( final Exception ex ) {
\r
2217 private void setMinNotCollapseBlValue( final double min_not_collapse_bl ) {
\r
2218 _min_not_collapse_bl = min_not_collapse_bl;
\r
2221 private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {
\r
2222 _min_not_collapse = min_not_collapse;
\r
2225 void setMsa( final Msa msa ) {
\r
2229 void setMsaFile( final File msa_file ) {
\r
2230 _msa_file = msa_file;
\r
2233 private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {
\r
2234 _phylogenetic_inference_options = phylogenetic_inference_options;
\r
2237 void setSeqs( final List<MolecularSequence> seqs ) {
\r
2241 void setSeqsFile( final File seqs_file ) {
\r
2242 _seqs_file = seqs_file;
\r
2245 private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
\r
2246 nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
\r
2247 nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
\r
2250 private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
\r
2251 nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
\r
2252 nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
\r
2253 nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() );
\r
2257 } // MainFrameApplication.
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git://source.jalview.org / jalview.git / blob